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https://github.com/alan-turing-institute/setvis
A tool for visualising set membership and patterns of missingness in data
https://github.com/alan-turing-institute/setvis
bokeh hut23 hut23-845 jupyter-notebook missing-data python set-visualization
Last synced: 2 days ago
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A tool for visualising set membership and patterns of missingness in data
- Host: GitHub
- URL: https://github.com/alan-turing-institute/setvis
- Owner: alan-turing-institute
- License: apache-2.0
- Created: 2021-07-02T12:41:40.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-10-29T18:18:37.000Z (17 days ago)
- Last Synced: 2024-10-29T20:24:37.065Z (17 days ago)
- Topics: bokeh, hut23, hut23-845, jupyter-notebook, missing-data, python, set-visualization
- Language: Python
- Homepage: https://setvis.readthedocs.io
- Size: 3.74 MB
- Stars: 4
- Watchers: 10
- Forks: 1
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
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README
# setvis
[](https://github.com/alan-turing-institute/setvis/actions/workflows/main.yml)
[](https://setvis.readthedocs.io/en/latest/?badge=latest)
Setvis is a python library for visualising set membership and patterns of missingness in data.
The plotting and interactive workflow of Setvis is designed for use within a Jupyter notebook (although it is possible to run outside Jupyter). The other components of Setvis can be used interactively or programmatically. The interactive plots are powered by [Bokeh](https://docs.bokeh.org/en/latest/index.html) widgets.
It operates on data using a memory efficient architecture, and supports loading data from flat files, Pandas dataframes, and directly from a Postgres database.
## Documentation
[The setvis documentation](https://setvis.readthedocs.io/en/latest/index.html) is hosted on Read the Docs.
## Installation (quick start)
**For the complete installation instructions, consult [the installation page of the documentation](https://setvis.readthedocs.io/en/latest/installation.html), which includes information on some extra installation options and setting up a suitable environment on several platforms.**
We recommend installing setvis in a python virtual environment or Conda environment.
To install setvis, most users should run:
```
pip install 'setvis[notebooks]'
```
This will include everything to run setvis in a notebook, and to run the tutorial examples that do not need a database connection.
The Bokeh plots produced by setvis require the package `notebook >= 6.4` to display properly. This will be included when installing setvis using the command above.
## Tutorials
For basic examples, please see the two example notebooks:
- [Missingness example](https://github.com/alan-turing-institute/setvis/blob/main/notebooks/Example%20-%20import%20data%20to%20visualize%20missingness.ipynb)
- [Set example](https://github.com/alan-turing-institute/setvis/blob/main/notebooks/Example%20-%20import%20data%20to%20visualize%20sets.ipynb)
Additionally, there is a series of Tutorials notebooks, starting with [Tutorial 1](https://github.com/alan-turing-institute/setvis/blob/main/notebooks/Tutorial%201%20-%20Overview%20and%20an%20example%20analysis.ipynb).
After installing setvis, to follow theses tutorials interactively you will need to clone or download this repository. Then start jupyter from within it:
```
python -m jupyter notebook notebooks
```
## Notice
The setvis software is released under the Apache Licence, version 2.0. See [LICENCE](./LICENCE) for details.
The data files [`./examples/datasets/simpsons - Format 1.csv`](https://github.com/alan-turing-institute/setvis/blob/main/examples/datasets/simpsons%20-%20Format%201.csv) and [`./examples/datasets/simpsons - Format 2.csv`](https://github.com/alan-turing-institute/setvis/blob/main/examples/datasets/simpsons%20-%20Format%202.csv), are based on a data file included in [UpSet](https://github.com/VCG/upset), copyright Visual Computing Group, Harvard, and distributed here under the terms of the MIT Licence.
The other data files in `./examples/datasets/` are released under the [Creative Commons Attribution 4.0 International Licence (CC-BY-4.0)](https://creativecommons.org/licenses/by/4.0/).
## Acknowledgements
The development of the setvis software was supported by funding from the Engineering and Physical Sciences Research Council (EP/N013980/1; EP/R511717/1) and the Alan Turing Institute.